I'm not an iPad guru by any means, but I just successfully backed out of a jailbreak by doing the following:

1. If you're planning on jailbreaking again, get PkgBackup or write down all your installed Cydia apps
2. Backup your iPad in iTunes (right-click on your device in the left pane and select Backup)
3. Restore your iPad to factory default in iTunes (left click on device in the left pane and select Restore, then choose Set up as New option)
4. Restore your iPad from backup (same as step 3, but select Restore from Backup rather than Set up as New)

You should then be back to where you were before, only no jailbreak. Probably a good idea to remove extra icons from the dock if you have Infinidock or otherwise prepare for going back to vanilla iPad from jailbreak. I'm not sure if those icons will be put back on the springboard or lost in the ether...I didn't want to test that myself. NOTE: all actions above are based on a Windows version of iTunes.

Sounds like you are doing the wrong type of restore. You seem to be choosing the "restore from backup" option. This is wrong. This option simply copies back your application settings and data from a backup file leaving the rest of your device intact.

You must plug in your iPad and press the big "Restore" button under the "Check for Update" button on the main summary screen.
That wipes your iPad and restores a factory fresh 4.2.1. There is absolutely no way the jailbreak can survive a full restore.

After you have done that you can re-sync with iTunes and if you want also "restore from backup" which will put your app settings back on the iPad. But your jailbreak and Cydia apps (if any) will be completely gone.

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